At least 43 people have been killed and several others remain missing after heavy rain and flash floods hit northern Pakistan close to the Afghan border.

Mosques, several houses and an army post in Ursoon village in the southwest of Chitral district in Khyber-Pakhtunkhwa province faced extensive damage after incessant rain caused flash floods early on Sunday.

Chitral is in the far north of Pakistan, bordering Afghanistan's Badakhshan province.

"Most bodies had been identified, however, some bodies might have been washed away to Afghanistan," Osama Ahmad Warraich, deputy commissioner of Chitral, told Al Jazeera, before adding that eight of the dead were soldiers.

Eighty-two homes in Ursoon were affected by the waters, a rescue services statement said, with some of them swept away, along with a mosque and an army post.

"Sixteen of the dead were offering prayers in the mosque when it was swept away by the flood," spokesperson for the provincial disaster management authority Latifur Rehman said.

The army has been taking part in rescue operations in the affected areas together with the district administration.

But Warraich said the bad weather was hampering rescue efforts, but added that authorities had "called for helicopters to join rescue operations" in the area.

Displaced families wait for relief in Chitral following the flash floods in Pakistan [EPA]

In April, rains and landslides killed at least 127 people in Khyber Pakhtunkhwa, Gilgit-Baltistan region and Pakistan-administered Kashmir.

Poorly-built homes across the country, particularly in rural areas, are susceptible to collapse during the annual spring and monsoon rains in July and August, which are often heavy.

During the rainy season last summer, torrential downpours and flooding killed at least 81 people and affected almost 300,000 people across Pakistan.

The worst flooding in recent times occurred in 2010, which covered almost a fifth of the country's total land mass, killing nearly 2,000 people and displacing some 20 million.